Reduced dimension plots {scater} | R Documentation |
Wrapper functions to create plots for specific types of reduced dimension results in a SingleCellExperiment object, or, if they are not already present, to calculate those results and then plot them.
plotPCASCE(object, ..., return_SCE = FALSE, draw_plot = TRUE, rerun = FALSE, ncomponents = 2, run_args = list()) plotTSNE(object, ..., return_SCE = FALSE, draw_plot = TRUE, rerun = FALSE, ncomponents = 2, run_args = list()) plotDiffusionMap(object, ..., return_SCE = FALSE, draw_plot = TRUE, rerun = FALSE, ncomponents = 2, run_args = list()) plotMDS(object, ..., ncomponents = 2, return_SCE = FALSE, rerun = FALSE, draw_plot = TRUE, run_args = list()) ## S4 method for signature 'SingleCellExperiment' plotPCA(object, ..., return_SCE = FALSE, draw_plot = TRUE, rerun = FALSE, ncomponents = 2, run_args = list())
object |
A SingleCellExperiment object. |
... |
Additional arguments to pass to |
return_SCE |
Logical, should the function return a SingleCellExperiment object with reduced dimension results in the |
draw_plot |
Logical, should the plot be drawn on the current graphics device?
Only used if |
rerun |
Logical, should the reduced dimensions be recomputed even if |
ncomponents |
Numeric scalar indicating the number of dimensions components to (calculate and) plot.
This can also be a numeric vector, see |
run_args |
Arguments to pass to |
Each function will search the reducedDims
slot for an appropriately named set of results and pass those coordinates onto plotReducedDim
.
If the results are not present or rerun=TRUE
, they will be computed using the relevant run*
function.
The result name and run*
function for each plot*
function are:
"PCA"
and runPCA
for plotPCA
"TSNE"
and runTSNE
for plotTSNE
"DiffusionMap"
and runDiffusionMap
for plotDiffusionMap
"MDS"
and runMDS
for "plotMDS"
Users can specify arguments to the run*
functions via run_args
.
If ncomponents
is a numeric vector, the maximum value will be used to determine the required number of dimensions to compute in the run*
functions.
However, only the specified dimensions in ncomponents
will be plotted.
A ggplot object or an SingleCellExperiment object, depending on return_SCE
.
Davis McCarthy, with modifications by Aaron Lun
runPCA
,
runDiffusionMap
,
runTSNE
,
runMDS
,
plotReducedDim
## Set up an example SingleCellExperiment data("sc_example_counts") data("sc_example_cell_info") example_sce <- SingleCellExperiment( assays = list(counts = sc_example_counts), colData = sc_example_cell_info ) example_sce <- normalize(example_sce) ## Examples plotting PC1 and PC2 plotPCA(example_sce) plotPCA(example_sce, colour_by = "Cell_Cycle") plotPCA(example_sce, colour_by = "Cell_Cycle", shape_by = "Treatment") plotPCA(example_sce, colour_by = "Cell_Cycle", shape_by = "Treatment", size_by = "Mutation_Status") ## Force legend to appear for shape: example_subset <- example_sce[, example_sce$Treatment == "treat1"] plotPCA(example_subset, colour_by = "Cell_Cycle", shape_by = "Treatment", by_show_single = TRUE) ## Examples plotting more than 2 PCs plotPCA(example_sce, ncomponents = 4, colour_by = "Treatment", shape_by = "Mutation_Status") ## Same for TSNE: plotTSNE(example_sce, perplexity = 10) ## Same for DiffusionMaps: plotDiffusionMap(example_sce) ## Same for MDS plots: plotMDS(example_sce)